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A method to track dataset reuse in biomedicine: Filtered GEO accession numbers in PubMed Central

Heather A Piwowar
2010 Proceedings of the American Society for Information Science and Technology  
Specifically, the full-text of papers stored in PubMed Central are queried for accession numbers of datasets archived in NCBI's Gene Expression Omnibus (GEO) repository.  ...  Automated portions of this method have been implemented in python and are openly available. Although imperfect, this dataset is a valuable initial resource for research into patterns of data reuse.  ...  ACKNOWLEDGMENTS This research was conducted under the auspices of DataONE, funded by a Cooperative Agreement through the NSF DataNET program (OCI-0830944).  ... 
doi:10.1002/meet.14504701450 fatcat:57z3hynpovarvh2yb7vimbid64

Open Data to Support CANCER Science—A Bioinformatics Perspective on Glioma Research

Fleur Jeanquartier, Claire Jean-Quartier, Sarah Stryeck, Andreas Holzinger
2021 Onco  
Our work aims to support and promote the use of publicly available resources in cancer research and demonstrates artificial intelligence (AI) methods to find answers to detailed questions.  ...  Supporting data sharing is paramount to making progress in cancer research.  ...  Pubmed Central (PMC) publication results on search for "open data cancer" per year, comparing the number of all results and filtered by open access. Author Contributions: Conceptualization, C.J.  ... 
doi:10.3390/onco1020016 fatcat:vn54hu3x3fhebfzxtee3c2z2fy

Data issues in the life sciences

Anne Thessen, David Patterson
2011 ZooKeys  
It relies on access to and reuse of data which will most likely have been generated to address other scientific problems.  ...  Access to a pool will invite "New" logic, strategies and tools (a "macroscope") to discover those trends, associations, discontinuities, and exceptions that reveal aspects of the underlying biology which  ...  The topics raised here were explored during a workshop held in Woods Hole, Massachusetts attended by computer, information and biological scientists, and representatives of academia, the private sector  ... 
doi:10.3897/zookeys.150.1766 pmid:22207805 pmcid:PMC3234430 fatcat:izhtzleyafd7pdwrbjrn63risa

Proceedings of the 6th International Symposium on Semantic Mining in Biomedicine (SMBM 2014)

S.N.
2014
The Research Programme on Biomedical Informatics (GRIB) is a node of the Spanish National Institute of Bioinformatics (INB).  ...  Acknowledgements We would like to thank Drs Tania Tudorache, Natasha Noy, and Matthew Horridge of Stanford University's Department of Biomedical Informatics for their valuable guidance in using the OWL  ...  These events are extracted using the Turku Event Extraction System (TEES) from 6,392,824 PubMed abstracts and 383,808 PubMed Central Open Access (OA) fulltext articles that were published up to 2012 and  ... 
doi:10.5167/uzh-98982 fatcat:avtlvr27hrdyfjfto47x2lfulu

The Fourth Paradigm – Data-Intensive Scientific Discovery [chapter]

Tony Hey
2012 Communications in Computer and Information Science  
The F o u r T H Data-In t e n s I v e scIen t I f I c DIs c o v e r y P a r a d i g m MiCroSoF T reSe arCH REDMOND, WASHINGTON  ...  Acknowledgments My thanks to the participants at the April 24, 2009, Buckland-Lynch-Larsen "Friday Seminar" on information access at the University of California, Berkeley, School of Information for a  ...  very helpful discussion on a draft of this material. to all the contributors to this book for sharing their visions within the Fourth Paradigm.  ... 
doi:10.1007/978-3-642-33299-9_1 fatcat:etue636ubrandga5corvkx3d7u

Information extraction from digital social trace data with applications to social media and scholarly communication data

Shubhanshu Mishra
2020 SIGIR Forum  
The thesis aims to act as a bridge between research questions and techniques used in DSTD from different domains.  ...  This identification allows us to utilize the graph structure of the data (e.g., user connected to a tweet, author connected to a paper, author connected to authors, etc.) for developing new information  ...  We use the citation information available from a collection of Web of Science PubMed citations, Microsoft Academic Graph [Sinha et al. 2015] and PubMed Central.  ... 
doi:10.1145/3451964.3451981 fatcat:36djwlckprhl5hymzhivrbnscu

EMBnet.journal 16 Suppl. A

EMBnet Journal
2010 EMBnet journal  
This is the first supplement from a conference and our plan is to continue to cover other conferences related to bioinformatics in action.  ...  This was an important occasion and we felt the need to document it properly. You now hold the result of this need in your hand. The first supplement ever published by EMBnet.journal.  ...  Acknowledgements and funding We acknowledge the support provided by UNAM (CTIC, CCG and IBt) for the overall conference, to EMBNet to support specific delegates, and from Acknowledgments We acknowledge  ... 
doi:10.14806/ej.16.a.156 fatcat:m3hkdlxdfzdovfgg7ke3xwygn4

Open Access Publishing: A Literature Review

Giancarlo F. Frosio
2014 Social Science Research Network  
106 For a discussion and collection of empirical data regarding the motivations, personal attributes and behavioural patterns of those who are engaged in producing free/libre and open source software (  ...  FLOSS), see Paul A David and Joseph Shapiro, 'Community-  ...  the biomedical field, major data aggregators -including PubMed, Index Medicus, PubMed Central and OVID -have open access databases and search platforms dedicated to open access material. 293 The leading  ... 
doi:10.2139/ssrn.2697412 fatcat:po3pq3dhebcebme3loceef2fgq

IMIA LaMB WG related event: Proceedings of 3rd International Conference on Biomedical Ontology, 2012, Graz

Ronald Cornet, Robert Stevens, Melanie Courtot, Trish Whetzel, Janna Hastings, Stefan Schulz, Ludger Jansen
2019 Zenodo  
This conference carried on the tradition of discussing medical ontologies, increasingly used in biology and medicine, and their use in annotation of both clinical and experimental data is now a common  ...  To be maximally effective, such ontologies must work well together. .... These conference addresses these problems.  ...  information to a Gene Ontology annotation.  ... 
doi:10.5281/zenodo.3381830 fatcat:pnndilxgzzbujnoqz7pytggtdi

International EcoHealth One Health Congress 2016

2016 EcoHealth  
The objective of this work was to analyze the association and economic impact of dengue cases near a hydroelectric construction area in Brazil.  ...  The methods presented a suggestive approach of HIA and included screening, scoping, appraisal of health impacts, economic valuation and recommendations.  ...  Efforts such as the US National Antibiotic Resistance Monitoring System (NARMS) track certain pathogens in humans and animals, but tend to include only a small number of pathogens, and not routinely produce  ... 
doi:10.1007/s10393-016-1182-0 pmid:27752838 fatcat:vq33qrth5rgjpkjxwnpx4fc4r4

Epigenomics of Cell Fate in Development and Disease

Rebecca Faith Lowdon
2016
I am grateful to my many friends in St. Louis and beyond who have supported me over the past five years.  ...  They have made a long journey a very enjoyable one. xi Above all, I thank my family, whose continuous love and support I treasure immensely.  ...  To isolate putatively functional noncoding SNVs in the COSMIC dataset, we took a stringent filtering approach (Figure 4 .2.a; Methods).  ... 
doi:10.7936/k7kw5dgm fatcat:vxde4uqhdzecffpilk2g2g2loi

Biomedical knowledge base construction from text and its applications in knowledge-based systems [article]

Patrick Ernst, Universität Des Saarlandes, Universität Des Saarlandes
2018
Following the fact-pattern duality paradigm and using a small number of seed facts for distant supervision of pattern-based extraction, we harvest a large number of fact candidates in an automated manner  ...  DeepLife integrates large KBs and harnesses entity linking methods to annotate articles in real-time in order to stay up-to-date on the latest health topics.  ...  publications: MEDLINE and PubMed Central database.  ... 
doi:10.22028/d291-27105 fatcat:ctjjzvcdnjantlzlzjfq4ayonq

The evaluation of ontologies: quality, reuse and social factors

Marzieh Talebpour
2020
Finding a "good" or the "right" ontology is a growing challenge in the ontology domain, where one of the main aims is to share and reuse existing semantics and knowledge.  ...  Before reusing an ontology, knowledge engineers not only have to find a set of appropriate ontologies for their search query, but they should also be able to evaluate those ontologies according to different  ...  filtering in this domain.  ... 
doi:10.26174/thesis.lboro.12287273 fatcat:ci7wazue5bdpnk7r4p6mn4rb3y

Appendix 143 Scientific Papers (full papers) A Novel Approach to Comprehensive Clinical Note Taking-from Concept to Product

Hinz Nz, Scott Pearson¹
unpublished
Successful OSS development projects have been found to have a specific set of features (see 3.1), and in addition an experienced commercial software partner may be necessary to orchestrate the software  ...  References The authors have experimented with the transformation of openEHRbased logical models, using jQVT and a tabular mapping of their elements to the UML Profile for CDA that is implemented in the  ...  They also provide the basis for datasets used to track outcomes and inform the allocation of resources.  ... 
fatcat:agvjkyjywbaazelp62nuzl54iq

Using logical entailments of gene annotations for biological discovery [article]

William Baumgartner
2021
Our method responds to past calls for enrichment methodologies to incorporate more than just the Gene Ontology, and in doing so we have addressed a number of the current challenges that face the field  ...  We present several methodologies that, when used collectively, vastly increase available gene annotations in both number and type.  ...  in biomedicine.  ... 
doi:10.25677/1fsc-th88 fatcat:hhdrrlxdvjbpdm53y3w2g64axu
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